Handbook. Influenza A H1N1 & H3N2 Real-TM. Real Time Amplification test for the detection of Influenza A H1N1 and H3N2 viruses

Transcription

1 Influenza A H1N1 & H3N2 Real-TM Handbook Real Time Amplification test for the detection of Influenza A H1N1 and H3N2 viruses REF V54-50FRT REF TV54-50FRT 50

2 NAME Influenza A H1N1 & H3N2 Real-TM INTENDED USE Influenza A H1N1 & H3N2 Real-TM is Real-Time amplification test for typing of Influenza virus A (identification to subtypes H1N1 and H3N2) RNA in Influenza virus cultures and in clinical material (nasal and oropharyngeal swabs; sputum, bronchial lavage, autopsy material). PRINCIPLE OF ASSAY Influenza A H1N1 & H3N2 Real-TM test is based on four major processes: isolation of Influenza A virus RNA from specimens, reverse transcription of the RNA and Real Time amplification of the cdna of Influenza A virus. Influenza A H1N1 & H3N2 Real-TM PCR kit is a qualitative test which contain the Internal Control (IC). It must be used in the isolation procedure in order to control the process of each individual sample extraction and serves also to identify possible reaction inhibition. MATERIALS PROVIDED Module No.1: Real Time PCR kit (V54-50FRT) Part N 2 Reverta-L : Reverse transcription of the RNA RT-G-mix-1, 5 x 0,01 ml; RT-mix, 5 x 0,125 ml; Reverse transcriptase (M-MLV), 0,03 ml; TE-buffer, 1,2 ml. Contains reagents for 60 tests. Part N 3 Influenza A Real-TM : Real Time amplification kit PCR-mix-1 H1N1, 55 tubes; PCR-mix-1 H3N2, 55 tubes; PCR-mix-2, 0,77 ml; Positive Control cdna H1N1 C+, 0,1 ml; Positive Control cdna H3N2 C+, 0,1 ml; DNA-buffer (NCA), 0,5 ml; Negative Control*, 1,2 ml; Internal Control (IC) RNA**, 5 x 0,12 ml; Internal Control (IC) DNA, 0,1 ml; Contains reagents for 55 tests. * must be used in the extraction procedure as Negative control of extraction. ** add 10 µl of Internal Control (IC) RNA during the RNA extraction procedure directly to the sample/lysis mixture (see extraction kit protocol)

3 Module No.2: Complete Real Time PCR test with RNA purification kit (TV54-50FRT) Part N 1 Ribo-Sorb : Sample preparation Lysis Solution, 22,5 ml; Washing Solution, 20 ml; Sorbent, 1,25 ml. RNA-eluent, 5 x 0,5ml; Contains reagents for 50 tests. Part N 2 Reverta-L : Reverse transcription of the RNA RT-G-mix-1, 5 x 0,01 ml; RT-mix, 5 x 0,125 ml; Reverse transcriptase (M-MLV), 0,03 ml; TE-buffer, 1,2 ml. Contains reagents for 60 tests. Part N 3 Influenza A Real-TM : Real Time amplification kit PCR-mix-1 H1N1, 55 tubes; PCR-mix-1 H3N2, 55 tubes; PCR-mix-2, 0,77 ml; Positive Control cdna H1N1 C+, 0,1 ml; Positive Control cdna H3N2 C+, 0,1 ml; DNA-buffer (NCA), 0,5 ml; Negative Control*, 1,2 ml; Internal Control (IC) RNA**, 5 x 0,12 ml; Internal Control (IC) DNA, 0,1 ml; Contains reagents for 55 tests. * must be used in the extraction procedure as Negative control of extraction. ** add 10 µl of Internal Control (IC) RNA during the RNA extraction procedure directly to the sample/lysis mixture (see extraction kit protocol)

4 MATERIALS REQUIRED BUT NOT PROVIDED Zone 1: sample preparation: RNA extraction kit (Module No. 1) Biosafety cabinet Desktop microcentrifuge for eppendorf type tubes Dry heat block Vortex mixer Pipettes Sterile pipette tips with aerosol barriers 1,5 ml polypropylene sterile tubes (Sarstedt, QSP, Eppendorf) Disposable gloves, powderless Tube racks 70% Ethanol (freshly prepared mixture of reagent grade 96% ethanol and distilled water) Acetone Refrigerator Freezer Zone 2: RT and amplification: Real Time Thermalcycler Workstation Pipettors (capacity 0,5-10 µl; 5-40 µl) with aerosol barrier Tube racks STORAGE INSTRUCTIONS Reverta-L must be stored at -20 C, Influenza A H1N1 & H3N2 Real-TM and Ribo-Sorb at 2-8 C. The kits can be shipped at 2-8 C for 3-4 days but should be stored at 2-8 C and -20 C immediately on receipt. STABILITY Influenza A H1N1 & H3N2 Real-TM is is stable up to the expiration date indicated on the kit label. The product will maintain performance through the control date printed on the label. Exposure to light, heat or humidity may affect the shelf life of some of the kit components and should be avoided. Repeated thawing and freezing of these reagents should be avoided, as this may reduce the sensitivity. QUALITY CONTROL In accordance with Sacace s ISO Certified Quality Management System, each lot is tested against predetermined specifications to ensure consistent product quality.

5 WARNINGS AND PRECAUTIONS The user should always pay attention to the following: Lysis Solution contains guanidine thiocyanate*. Guanidine thiocyanate is harmful if inhaled, or comes into contact with skin or if swallowed. Contact with acid releases toxic gas. (Xn; R: 20/21/22-36/37/38; S: 36/37/39). Clinical specimens from suspect influenza A (H1N1) cases should be performed in a BSL2 laboratory with BSL3 practices (enhanced BSL2 conditions). Use sterile pipette tips with aerosol barriers and use new tip for every procedure. Store extracted positive material (samples, controls and amplicons) away from all other reagents and add it to the reaction mix in a separate area. Thaw all components thoroughly at room temperature before starting an assay. When thawed, mix the components and centrifuge briefly. Use disposable gloves, laboratory coats and eye protection when handling specimens and reagents. Thoroughly wash hands afterwards. Do not eat, drink, smoke, apply cosmetics, or handle contact lenses in laboratory work areas. Do not use a kit after its expiration date. Dispose of all specimens and unused reagents in accordance with local authorities regulations. Specimens should be considered potentially infectious and handled in a biological cabinet in accordance with appropriate biosafety practices. Clean and disinfect all sample or reagent spills using a disinfectant such as 0.5% sodium hypochlorite, or other suitable disinfectant. Avoid sample or reagent contact with the skin, eyes, and mucous membranes. If skin, eyes, or mucous membranes come into contact, rinse immediately with water and seek medical advice immediately. Material Safety Data Sheets (MSDS) are available on request. Use of this product should be limited to personnel trained in the techniques of DNA amplification. The laboratory process must be one-directional, it should begin in the Extraction Area and then move to the Amplification and Detection Areas. Do not return samples, equipment and reagents to the area in which the previous step was performed. Some components of this kit contain sodium azide as a preservative. Do not use metal tubing for reagent transfer. * Only for Module No.2

6 PRODUCT USE LIMITATIONS All reagents may exclusively be used in in vitro diagnostics. Use of this product should be limited to personnel trained in the techniques of DNA amplification (UNI EN ISO :2012). Strict compliance with the user manual is required for optimal PCR results. Attention should be paid to expiration dates printed on the box and labels of all components. Do not use a kit after its expiration date. SAMPLE COLLECTION, STORAGE AND TRANSPORT Influenza A H1N1 & H3N2 Real-TM can analyze RNA extracted from: Human diagnostics: mucosal swabs ( nasal, oral): swab area and place in Eppendorf tube with 0,5 ml of saline water or PBS sterile. Agitate vigorously. Repeat the swab and agitate in the same tube. Centrifuge at 1000g/min for 5 min. Remove and discard the supernatant. Resuspend the pellet in 100 µl of Saline water. bronchial lavage, nasal wash: centrifuge at 2000 g/min for min. If the pellet is not visible add 10 ml of liquid and repeat centrifugation. Remove and discard the supernatant. Resuspend the pellet in 100 µl of Saline water. autopsy material: Collect autopsy material into sterile containers and freeze immediately or analyze within 1 h. The samples can be stored at 68 C for 1 year. Homogenize the samples using sterile porcelain mortars and pestles and then prepare 10 % suspension in sterile saline or PBS. Transfer the suspension into a 1.5-ml tube and centrifuge at rpm for 5 min. Use 100 µl of the supernatant for RNA extraction. Freeze the rest of aspirate if it is necessary to repeat analysis later. Animal diagnostics: feces: o Prepare the 10% suspension of feces (4-5 g) with Saline solution. Vortex to get a homogeneous suspension and incubate for 10 min at room temperature. Transfer the supernatant in the sterile 1,5 ml polypropylene tube and centrifuge for 5 min to g. Use the supernatant for RNA extraction. animals feeds and feeds for poultry: homogenized with mechanical homogenizer or scalpel, glass sticks, teflon pestles cloaca swabs: resuspend in 1,0 ml of saline water or PBS sterile and centrifuge at g/min for 10 min. Remove and discard the supernatant. Resuspend the pellet in 100 µl of Saline water.

7 tissue: 1,0 gr (parenchimatous organs, trachea, lung, brain) homogenized with mechanical homogenizer or scalpel, glass sticks, teflon pestles and dissolved in 1,0 ml of saline water or PBS sterile. Vortex vigorously and incubate 30 min at room temperature. Transfer the supernatant into a new 1,5 ml tube; Specimens can be stored at +2-8 C for no longer than 12 hours, or frozen at -20 C to -80 C. Transportation of clinical specimens must comply with country, federal, state and local regulations for the transport of etiologic agents. RNA ISOLATION Sacace Biotechnologies recommends to use the following kits: Ribo-Sorb- (Sacace, REF K-2-1); DNA/RNA-Prep (Sacace, REF K-2-9); SaMag Viral Nucleic Acids Extraction kit (Sacace, REF SM003); Please carry out the RNA extraction according to the manufacturer s instructions. Add 10 µl of Internal Control during the DNA isolation procedure directly to the sample/lysis mixture. SPECIMEN AND REAGENT PREPARATION 1. Lysis Solution and Washing Solution (in case of their storage at +2-8 о С) should be warmed up to о С until disappearance of ice crystals. Prepare required quantity of 1.5 ml polypropylene tubes including one tube for Negative Control of Extraction. 2. Add to each tube 450 µl Lysis Solution and 10 µl Internal Control (IC RNA). Mix by pipetting and incubate 5 min at room temperature. 3. Add 100 µl of samples to the appropriate tube containing Lysis Solution and IC. 4. Prepare Controls as follows: add 100 µl of C Negative Control to the tube labeled Cneg 5. Vortex the tubes and centrifuge for 5 sec at 5000g. If the sample is not completely dissolved it is recommended to re-centrifuge the tube for 1 min at a maximum speed ( g.) and transfer the supernatant into a new tube for RNA extraction 6. Vortex vigorously Sorbent and add 25 µl to each tube. 7. Vortex for 5-7 sec and incubate all tubes for 10 min at room temperature. Vortex periodically. 8. Centrifuge all tubes for 1 min at 10000g and using a micropipette with a plugged aerosol barrier tip, carefully remove and discard supernatant from each tube without disturbing the pellet. Change tips between tubes.

8 9. Add 400 µl of Washing Solution to each tube. Vortex vigorously, centrifuge for 1 min at 10000g. and using a micropipette with a plugged aerosol barrier tip, carefully remove and discard supernatant from each tube without disturbing the pellet. Change tips between tubes. 10. Add 500 µl of Etanolo al 70% to each tube. Vortex vigorously, centrifuge for 1 min at 10000g. and using a micropipette with a plugged aerosol barrier tip, carefully remove and discard supernatant from each tube without disturbing the pellet. Change tips between tubes. 11. Repeat step Add 400 µl of Acetone to each tube. Vortex vigorously, centrifuge for 1 min at 10000g and using a micropipette with a plugged aerosol barrier tip, carefully remove and discard supernatant from each tube without disturbing the pellet. Change tips between tubes. 13. Incubate all tubes with open cap for 10 min at 60 C. 14. Resuspend the pellet in 40 µl of RNA-eluent. Incubate for 10 min at 60 C and vortex periodically. Centrifuge the tubes for 2 min at maximum speed ( g). 15. The supernatant contains RNA ready for use. The RT-PCR can be performed the same day. If this is not possible, the RNA preparations can be stored at -80 C for up to one month. RT AND AMPLIFICATION Reverse Transcription: 1) Prepare Reaction Mix: for 12 reactions, add 5,0 µl RT-G-mix-1 into the tube containing RTmix and vortex for at least 5-10 seconds, centrifuge briefly. This mix is stable for 1 month at -20 C. Add 6 µl M-MLV into the tube with Reagent Mix, mix by pipetting, vortex for 3 sec, centrifuge for 5-7 sec (must be used immediately after the preparation). (If it is necessary to test less than 12 samples add for each sample (N) in the new sterile tube 10*N µl of RT-G-mix-1 with RT-mix and 0,5*N µl of M-MLV). 2) Add 10 µl of Reaction Mix into each sample tube. 3) Pipette 10 µl RNA samples to the appropriate tube. (If the Ribo-Sorb isolation kit is used as a RNA extraction kit, re-centrifuge all the tubes with extracted RNA for 2 min at maximum speed ( g) and take carefully supernatant. N.B. don t disturb the pellet, sorbent inhibit reaction).carefully mix by pipetting. 4) Place tubes into thermalcycler and incubate at 37 o С for 30 minutes. 5) Dilute 1: 2 each obtained cdna sample with TE-buffer (add 20 µl TE-buffer to each tube). cdna specimens could be stored at -20 o С for a week or at -70 o С during a year.

9 PCR-mix-1 1- H1N1 PCR-mix- PCR-mix- 1- H3N2 PCR Reagents preparation Reaction Mix 25 µl 1) Prepare the required number of tubes with PCR-mix-1 H1N1 (or PCR-mix-1 H3N2) for amplification of cdna from clinical and control samples. Make sure that wax completely covers the solution at the bottom. 2) Add 7 µl of PCR-mix-2 to the surface of the wax layer of each tube ensuring that it does not fall under the wax. 3) Add 10 µl of cdna obtained from clinical or control samples at the reverse transcription stage to the prepared tubes. 4) Carry out the control amplification reactions: NCA - Add 10 µl of TE-buffer to the tube labeled NCA (Negative control of amplification). C+A H1N1 - Add 10 µl of Positive Control cdna Influenza virus A H1N1 to the tube labeled C+A H1N1 (Positive control of amplification). C+A H3N2 - Add 10 µl of Positive Control cdna Influenza virus A H3N2 to the tube IC DNA Pos labeled C+A H3N2 (Positive control of amplification). - Add 10 µl of Positive Control STI to the tube labeled IC DNA Pos (Positive control of amplification). Create a temperature profile on your Real-time instrument as follows: Stage Тemp, С Time Fluorescence detection Cycle repeats Hold 95 5 min s Cycling s s s Cycling s FAM(Green), HEX/JOE(Yellow), ROX(Orange) s For example SaCycler-96 (Sacace), CFX96/iQ5 TM (Biorad), Mx3000P/3005P TM (Agilent); Rotor-Gene 3000/6000/Q (Corbett Research, Qiagen) INSTRUMENT SETTINGS Rotor-type instruments Calibrate/Gain More Settings/ Channel Threshold Slope Correct Optimisation Outlier Removal FAM/Green from 5 Fl to 10 Fl % off JOE/Yellow from 4 Fl to 8 Fl % off Rox/Orange from 4 Fl to 8 Fl % on FAM/Green from 5 Fl to 10 Fl % off JOE/Yellow from 4 Fl to 8 Fl % off Rox/Orange from 4 Fl to 8 Fl % on

10 RESULTS ANALYSIS The results are interpreted by the device software through the presence of crossing of fluorescence curve with the threshold line. Channels for detection of gene targets PCR-mix-1 Detection in channel FAM/Green JOE/HEX/Yellow ROX/Orange/Texas Red PCR-mix-1- H1N1 IC Influenza virus A H1 Influenza virus A N1 PCR-mix-1- H3N2 IC Influenza virus A H3 Influenza virus A N2 Results are accepted as relevant if both positive and negative controls of amplification are passed. Analysis of results for clinical samples: - AH1 (or A/H3) Influenza virus is detected in a sample if the Ct value is detected in the JOE/Yellow channel. - AN1 (or A/N2) Influenza virus is detected in a sample if the Ct value is detected in the ROX/Orange channel. - If Ct value is not detected in one or both channels (JOE/Yellow or ROX/Orange) and the Ct value for the Internal Control is less than the Ct value specified for the IC (see table Results for controls) in the FAM/Green channel, the analyzed A/H1N1 (or A/H3N2) subtype of the epidemic Influenza virus is not found. Results for controls Control Negative Control DNAbuffer IC DNA C+1, C+2 Stage for control RNA extraction Amplification Amplification Ct value in channels FAM Green JOE Yellow/HEX ROX/Orange/ Texas Red Interpretation Pos (< 30) Neg Neg OK Neg Neg Neg OK Pos (< 30) Neg Neg OK Amplification Neg Pos (< 25) Pos (< 25) OK PERFORMANCE CHARACTERISTICS The kit Influenza A H1N1 & H3N2 Real-TM allows to detect Influenza A in 100% of the tests with a sensitivity of not less than 1000 copies/ml.

11 TROUBLESHOOTING 1. Weak or absent signal of the IC (Fam/Green channel): retesting of the sample is required. The PCR was inhibited. Make sure that you use a recommended RNA extraction method and follow the manufacturer s instructions. Re-centrifuge all the tubes before pipetting the extracted RNA for 2 min at maximum speed ( g) and take carefully supernatant. Don t disturb the pellet, sorbent inhibit reaction. The reagents storage conditions didn t comply with the instructions. Check the storage conditions The PCR conditions didn t comply with the instructions. Check the PCR conditions and for the IC detection select the fluorescence channel reported in the protocol. The IC was not added to the sample during the pipetting of reagents. Make attention during the RNA extraction procedure. 2. Weak signal on the Fam(Green) (Ct > 30), Joe (Yellow)/Cy3/HEX (Ct > 35) or Rox (Orange)/TexasRed channel (Ct > 35): retesting of the sample is required. 3. Any signal with Negative PCR Control. Contamination during PCR preparation procedure. All samples results are invalid. Decontaminate all surfaces and instruments with sodium hypochlorite and ethanol or special DNA decontamination reagents. Pipette the Positive controls at the end. Repeat the PCR preparation with the new set of reagents.

12 KEY TO SYMBOLS USED List Number Caution! Lot Number Contains sufficient for <n> tests RUO For Research Use Only Version Store at Manufacturer Consult instructions for use NCA NCE C+ Negative Control of Amplification Negative control of Extraction Positive Control of Amplification Expiration Date IC Internal Control * SaCycler is a registered trademark of Sacace Biotechnologies * Rotor-Gene is a registered trademark of Qiagen * CFX and iq5 are registered trademarks of Bio-Rad Laboratories * MX 3000P/3005P is a registered trademark of Agilent Technologies Sacace Biotechnologies Srl via Scalabrini, Como Italy Tel Fax mail: info@sacace.com web: